Predict Protein Structures with AlphaFold on Vertex AI
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Today, to accelerate research in the bio-pharma space, from the creation of treatments for diseases to the production of new synthetic biomaterials, we are announcing a new Vertex AI solution that demonstrates how to use Vertex AI Pipelines to run DeepMind’s AlphaFold protein structure predictions at scale.
Once a protein’s structure is determined and its role within the cell is understood, scientists can develop drugs that can modulate the protein function based on its role in the cell. DeepMind, an AI research organization within Alphabet, created the AlphaFold system to advance this area of research by helping data scientists and other researchers to accurately predict protein geometries at scale.
In 2020, in the Critical Assessment of Techniques for Protein Structure Prediction (CASP14) experiment, DeepMind presented a version of AlphaFold that predicted protein structures so accurately, experts declared the “protein-folding problem” solved. The next year, DeepMind open sourced the AlphaFold 2.0 system. Soon after, Google Cloud released a solution that integrated AlphaFold with Vertex AI Workbench to facilitate interactive experimentation. This made it easier for many data scientists to efficiently work with AlphaFold, and today’s announcement builds on that foundation.
Last week, AlphaFold took another significant step forward when DeepMind, in partnership with the European Bioinformatics Institute (EMBL-EBI), released predicted structures for nearly all cataloged proteins known to science. This release expands the AlphaFold database from nearly 1 million structures to over 200 million structures—and potentially increases our understanding of biology to a profound degree. Between this continued growth in the AlphaFold database and the efficiency of Vertex AI, we look forward to the discoveries researchers around the world will make.
In this article, we’ll explain how you can start experimenting with this solution, and we’ll also survey its benefits, which include offering lower costs through optimized selection of hardware, reproducibility through experiment tracking, lineage and metadata management, and faster run time through parallelization.
Background for running AlphaFold on Vertex AI
Generating a protein structure prediction is a computationally intensive task. It requires significant CPU and ML accelerator resources and can take hours or even days to compute. Running inference workflows at scale can be challenging—these challenges include optimizing inference elapsed time, optimizing hardware resource utilization, and managing experiments.Our new Vertex AI solution is meant to address these challenges.
To better understand how the solution addresses these challenges, let’s review the AlphaFold inference workflow:
- Feature preprocessing. You use the input protein sequence (in the FASTA format) to search through genetic sequences across organisms and protein template databases using common open source tools. These tools include JackHMMER with MGnify and UniRef90, HHBlits with Uniclust30 and BFD, and HHSearch with PDB70. The outputs of the search (which consist of multiple sequence alignments (MSAs) and structural templates) and the input sequences are processed as inputs to an inference model. You can run the feature preprocessing steps only on a CPU platform. If you’re using full-size databases, the process can take a few hours to complete.
- Model inference. The AlphaFold structure prediction system includes a set of pretrained models, including models for predicting monomer structures, models for predicting multimer structures, and models that have been fine-tuned for CASP. At inference time, you independently run the five models of a given type (such as monomer models) on the same set of inputs. By default, one prediction is generated per model when folding monomer models, and five predictions are generated per model when folding multimers. This step of the inference workflow is computationally very intensive and requires GPU or TPU acceleration.
- (Optional) Structure relaxation. In order to resolve any structural violations and clashes that are in the structure returned by the inference models, you can perform a structure relaxation step. In the AlphaFold system, you use the OpenMM molecular mechanics simulation package to perform a restrained energy minimization procedure. Relaxation is also very computationally intensive, and although you can run the step on a CPU-only platform, you can also accelerate the process by using GPUs.
The Vertex AI solution
The AlphaFold batch inference with the Vertex AI solution lets you efficiently run AlphaFold inference at scale by focusing on the following optimizations:
- Optimizing inference workflow by parallelizing independent steps.
- Optimizing hardware utilization (and as a result, costs) by running each step on the optimal hardware platform. As part of this optimization, the solution automatically provisions and deprovisions the compute resources required for a step.
- Describing a robust and flexible experiment tracking approach that simplifies the process of running and analyzing hundreds of concurrent inference workflows.
The following diagram shows the architecture of the solution.
The solution encompasses the following:
A strategy for managing genetic databases. The solution includes high-performance, fully managed file storage. In this solution, Cloud Filestore is used to manage multiple versions of the databases and to provide high throughput and low-latency access.
An orchestrator to parallelize, orchestrate, and efficiently run steps in the workflow. Predictions, relaxations, and some feature engineering can be parallelized. In this solution, Vertex AI Pipelines is used as the orchestrator and runtime execution engine for the workflow steps.
Optimized hardware platform selection for each step. The prediction and relaxation steps run on GPUs, and feature engineering runs on CPUs. The prediction and relaxation steps can use multi-GPU node configurations. This is especially important for the prediction step because the memory usage is approximately quadratic with the number of residues. Therefore, predicting a large protein structure can exceed the memory of a single GPU device.
Metadata and artifact management. The solution includes management for running and analyzing experiments at scale. In this solution, Vertex AI Metadata is used to manage metadata and artifacts.
The basis of the solution is a set of reusable Vertex AI Pipelines components that encapsulate core steps in the AlphaFold inference workflow: feature preprocessing, prediction, and relaxation. In addition to those components, there are auxiliary components that break down the feature engineering step into tools, and helper components that aid in the organization and orchestration of the workflow.
The solution includes two sample pipelines: the universal pipeline and a monomer pipeline. The universal pipeline mirrors the settings and functionality of the inference script in the AlphaFold Github repository. It tracks elapsed time and optimizes compute resources utilization. The monomer pipeline further optimizes the workflow by making feature engineering more efficient. You can customize the pipeline by plugging in your own databases.
Next steps
To learn more and to try out this solution, check our GitHub repository, which contains the components and universal and monomer pipelines. The artifacts in the repository are designed so that you can customize them. In addition, you can integrate this solution into your upstream and downstream workflows for further analysis. To learn more about Vertex AI, visit our product page.
Acknowledgements
We would like to thank the following people for their collaboration: Shweta Maniar, Sampath Koppole, Mikhail Chrestkha, Jasper Wang, Alex Burdenko, Meera Lakhavani, Joan Kallogjeri, Dong Meng (NVIDIA), Mike Thomas (NVIDIA), and Jill Milton (NVIDIA).
Finally and most importantly, we would like to thank our Solution Manager Donna Schut for managing this solution from start to finish. This would not have been possible without Donna.
How TapClicks’ Google Cloud Migration Makes Life Easy for Marketers
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Editor’s note: In this blog post we learn how TapClicks migrated to Google Cloud to offer their marketing customers a unified platform for data management, operations, insights, and analysis.
TapClicks is a smart marketing cloud, powered by data, that unifies our customer’s marketing. By choosing to migrate our core applications last year to Google Cloud, we cut costs, solved data-sharing concerns for our customers, and opened our stack up to a new ecosystem of possibilities.
The core problem that we’re solving for our customers is how to manage their marketing infrastructures data and operations. Life isn’t easy for marketers now. There are 7,000 different vendors servicing this space today – creating much complexity between digital agencies, media, and brands. Marketers face challenges in navigating all of these systems, logging in and out, understanding pacing goals, and managing the flow of marketing data so they can analyze and report internally as well as to their clients at scale.
We unify omnichannel campaign data (250 API connectors and 6000 Smart Connectors ™ ) from a plethora of marketing sources on an automated data warehousing solution, creating simplicity for organizations. Over 4,000 agencies, media companies, and brands use our Marketing Operations and Data Management Platform, which imports data at scale and creates an automatic data warehouse on Google Cloud. Teams can also leverage TapClicks, like our world class Facebook connector, to import data directly into Google Data Studios. Beyond importing and storing, we also provide data exporting to other Google solutions like Google Data Studio and Google Sheets. We also create interactive dashboards that let stakeholders and clients analyze their data, as well as automated, multi-channel reports that go out to clients at specified times. So channel comparisons, optimizations, attribution, and calculations are easily performed. Some of our customers are able to generate hundreds of thousands of individual reports and dashboards for their clients.
Although we may be best known for our reporting and analytics, we also empower teams managing the marketing operations workflow from customers and internal stakeholders, especially at scale. Our user-friendly, configurable system helps manage their orders and campaigns. Through automation of this process, we deliver tremendous amounts of efficiency, time saving, cost savings, and reduction of errors. The combination of these solutions makes up our unified platform, with additional capabilities like marketing intelligence that offers competitive and brand-level analysis. This is a disruptive solution in use by all leading media companies, agencies and many brands.
Partnering for possibilities
We faced a few challenges with our original tech stack, which included a mix of the leader in web services revenue, leaders in high performance data warehousing, as well as vendors on bare metal servers.
- One challenge was around costs, which were growing.
- Second, many of our customers work with multiple brands, and are very hesitant to share their data with the leader in web services, who’s often viewed as their competitor.
- Third, these vendors are more focused on their own revenue rather than a true long term partnership that would enable their customers to enjoy similar success as they have experienced.
When looking at other cloud providers, Google Cloud emerged for us as the front runner. They were competitive on costs, and their native Kubernetes support was superior— a big selling point for our DevOps team. There’s also a movement in the marketing and advertising industry away from AWS toward Google Cloud because of the data-sharing concern. Finally, most of our customers are already using Google Cloud tools, so there’s brand recognition and familiarity there, and easier integrations with their own systems.
Migrating to Google Cloud
Our migration, which took about five months, involved moving a significant chunk of our infrastructure, including our core applications, using Google Kubernetes Engine (GKE). In our legacy architecture, each of our clients was assigned to one of our virtual machines (VMs), and there was a lot of unused capacity because we had to provision for the max usage. We appreciated GKE’s cloud native capabilities, especially autoscaling, a huge benefit for our web application. We have varying usage patterns during the day, and though our application is mostly used during business hours, there are also days in the month of higher usage, and autoscaling saves us time and costs. GKE also makes deployments much easier, and we anticipate a lot of benefits there for our developer environments. We’ve moved some of our microservices into GKE and plan to move more in the future. All in all, we were able to migrate our core products and the bulk of our AWS spend successfully to Google Cloud.
We also moved from our other vendors Relational Database Service (RDS) to running MySQL on our own VMs on Google Cloud, which gives us more flexibility in terms of settings and fine tuning. We’re still trying to find the best mix as we’re modernizing our infrastructure, and we took this opportunity to migrate from MySQL 5.7 to 8.0.
Our next stage is exploring more of the capabilities and services of Google Cloud, including BigQuery, which we’re considering for our own data warehouse. The fact that we could also run Snowflake on Google Cloud, if needed, was another selling point for our migration.
We’re especially interested in BigQuery ML’s machine learning and natural language processing capabilities, which enabled better predictive insights. Our customers want insights from their campaigns— which are working, which are paying off, where should they invest next? Using our platform, they’re looking not only to generate reporting, but also identify opportunities to improve campaign performance. We plan to use AI and ML to improve those capabilities, so that our customers can seamlessly unlock insight and intelligence from their marketing data and campaigns.
Double-clicking on Google Cloud
For us, being able to deeply leverage and partner with Google Cloud to deliver those solutions on a single stack is critical, and we think our customers will love it. We see TapClicks and Google Cloud partnering at a level beyond what you typically see in a cloud provider relationship. Already, fifty percent of our company is working with various Google Cloud solutions, and we envision TapClicks and Google Cloud as extensions of each other, providing a single, powerful platform solution.
Google Cloud understands the partnership concept, and their team was able to shine a light on their services and what they could bring to the table. Compared to our previous experiences, dealing with the Google Cloud team has been a true pleasure. Now that we’ve migrated, we’re ready to take our next steps into the services available to us in the Google Cloud ecosystem, and the problems we’ll continue to solve for our customers. Learn more about TapClicks and BigQuery ML.
Revolutionizing Generative AI Applications with Google’s Vertex AI
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At Google Cloud, we’re committed to making generative AI useful for everyone. Doing so requires more than making powerful foundation models available to businesses, governments, and developers. Models also need to be backed by platforms that make adoption faster and safer, with onramps to meet organizations wherever they are, regardless of their software or data science expertise.
Today, we’re excited to announce general availability of Generative AI support on Vertex AI, giving customers access to our latest platform capabilities for building and powering custom generative AI applications. With this update, developers can access our text model powered by PaLM 2, Embeddings API for text, and other foundation models in Model Garden, as well as leverage user-friendly tools in Generative AI Studio for model tuning and deployment. Backed by enterprise-grade data governance, security, and safety features, Vertex AI can make it easier than ever for customers to access foundation models, customize them with their own data, and quickly build generative AI applications.
Vertex AI powers generative AI model customization for enterprise developers, data scientists, and everyone in between
Foundation models are the starting point for creating customized generative AI applications—but models alone are not sufficient. That’s why in March, we announced Generative AI support on Vertex AI, the biggest-ever update to our machine learning platform, and began working with trusted testers. Now generally available to customers, Model Garden and Generative AI Studio leverage Google Cloud’s tight partnership with Google Research and Google DeepMind, making it easy for developers and data scientists to use, customize, and deploy models.
Model Garden lets customers access and experiment with foundation models from Google and its partners, with over 60 models available and many more to come. In addition to making Model Garden, PaLM 2, and Embeddings API for text generally available, we’re also making our recently-announced Codey model for code completion, generation, and chat available for public preview.
Along with these and other foundation models, Vertex AI offers a full ecosystem of tools to help builders tune, deploy, and govern models in production. For example, in May, we were the first enterprise ML platform to provide Reinforcement Learning with Human Feedback, or RLHF, which helps improve model usefulness and reduce cost. We’ve also upgraded Vertex AI’s suite of MLOps tools for model development and maintenance for customers who need to manage large models. With Generative AI Studio generally available, customers can now leverage an even wider range of tools, including multiple tuning methods for large models, that can significantly accelerate development of custom generative AI applications.
We’re already seeing innovative results from early adopters via our trusted tester program and preview period. For example, leading global airline supplier GA Telesis is using our PaLM model on Vertex AI to build a data extraction solution that automatically synthesizes email orders and provides customers a quote. This eliminates the need for their sales teams to manually cross-reference emails with inventory availability. GitLab is leveraging our Codey model on Vertex AI for their “Explain this Vulnerability” feature, which gives their users a natural language description of code vulnerabilities, along with recommendations for resolving them. Canva, the visual communication platform, is using Google Cloud’s rich generative AI capabilities in language translation to better support its non-English speaking users, letting users easily translate presentations, posters, social media posts, and more into over a hundred languages. The company is also testing ways that Google’s PaLM technology can turn short video clips into longer, more compelling stories.
And today, we’re pleased to share that Typeface, and DataStax are also building new generative AI capabilities with Vertex AI.
Now is the time to build
These announcements add to our news yesterday that we’ve added expanded access to Enterprise Search on Generative AI App Builder (Gen App Builder), allowing businesses to create custom chatbots and search engines that combine generative AI with Google’s semantic search technologies. Gen App Builder offers out-of-box solutions to common generative AI use cases, Vertex AI’s expansive platform capabilities can accelerate wide-ranging innovation, and growing ecosystem support from partners help our customers build freely. Together, these technologies and partnerships mean the full spectrum of developers and data scientists, from novices to seasoned experts, can build generative AI apps with enterprise-ready services on Google Cloud.
As with our entire Cloud portfolio, Vertex AI and Gen App Builder help give customers complete control over their data; it doesn’t need to leave the customer’s tenant, is encrypted both in transit and at rest, and is not shared or used to train Google models. Google rigorously evaluates our new models to ensure they meet our Responsible AI Principles, and all of our generative AI offerings include the user security, data management, and access controls Google Cloud customers have come to expect.
We’re grateful to our trusted testers for their integral role in bringing Generative AI support on Vertex AI to market, and we look forward to seeing what customers across all industries create with our growing catalog. To learn more about Google Cloud’s generative AI products, visit our solutions page, and to keep up with our latest AI news, don’t miss “The Prompt” or our generative AI primer for executives on Transform with Google Cloud.
Google AppSheet Leads the Low-code Development Platform Market for Business Developers: Forrester
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We’re excited to share the news that leading global research and advisory firm Forrester Research has named Google AppSheet a Leader in the recently released report The Forrester Wave™: Low-code Platforms for Business Developers, Q4 2021. It’s our treasured community of business developers—those closest to the challenges that line-of-business apps can solve—who deserve credit for not only the millions of apps created with AppSheet, but also the collaborative approach to no-code development that has helped further our mission of empowering everyone to build custom solutions to reclaim their time and talent.
AppSheet received the highest marks possible in the product vision and planned enhancements criteria, with Forrester noting in the report that “AppSheet’s vision for AI-infused-and-supported citizen development is unique and particularly well suited to Google. The tech giant’s deep pockets and ecosystem give AppSheet an advantage in its path to market, market visibility, and product roadmap.”
“Features for process automation and AI are leading,” remarking that, “The platform provides a clean, intuitive modeling environment suitable for both long-running processes and triggered automations, as well as a useful range of pragmatic AI services such as document ingestion.”
Many enterprise customers including Carrefour Property – Carmila, Globe Telecom, American Electric Power, and Singapore Press Holdings (SPH) choose AppSheet as their business developer partner, along with thousands of other organizations in every industry. We are honored to serve these customers and to be a Leader in the Forrester Wave™: Low-code Platforms for Business Developers. We look forward to continuing to innovate and to helping customers on their digital transformation journey. To download the full report, visit here and enter your email address. To learn more about AppSheet, visit our website.
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AI has the power to revolutionize every industry—from retail to agriculture, and education to healthcare. Yet many businesses still haven’t begun to adopt AI.
There are a number of factors, including the need for specialized talent and hardware, the right types and quantities of data for training and refining machine learning models, and of course, the broader complexities of introducing a new way of working inside an organization.
But above all, AI can be challenging to apply to very specific business needs.
Google wants to change that, which is why it’s introducing a number of AI solutions aimed at making it easier for businesses to use AI to address many of these specific use cases.
Google’s AI solutions fall into two categories. The first is a set of pre-packaged AI solutions that can be easily integrated into existing workflows. To make these solutions as easy to implement as possible, Google works with popular, trusted enterprise partners who have deep-domain expertise in these workflows.
The majority of Google’s pre-packaged solutions will be delivered through these partners, although it will be offering some
The second category of AI solutions is comprised of reference architectures that businesses can use to create highly-custom AI tools. These require more development work than Google’s pre-packaged
Additionally, businesses can build on these architectures and deploy them to market more quickly, helping your business take advantage of AI, faster.
Learn more about all Google’s AI solutions. Download the whitepaper now!
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How Marketers Can Turn Information into Action with Machine Learning
The biggest challenge marketers face with machine learning is, “how to get starter”? Instead of getting overwhelmed, they should focus on the applied machine learning by using the algorithms that are already built.
Cassie Kozyrkov, the chief decision scientist with Google Cloud, says that marketers who are overwhelmed by everything they’re hearing about machine learning should focus on key ingredients, not building an entire kitchen.
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